AutoCloner

Multiple sequence alignment - TraesCS5B01G390100

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS5B01G390100	chr5B	100.000	7488	0	0	1	7488	569243368	569250855	0.000000e+00	13828.0
1	TraesCS5B01G390100	chr5B	96.752	7512	173	23	1	7488	569142191	569149655	0.000000e+00	12454.0
2	TraesCS5B01G390100	chr5B	85.145	5123	707	42	1219	6308	454865651	454870752	0.000000e+00	5195.0
3	TraesCS5B01G390100	chrUn	87.062	5109	626	25	1219	6308	111007462	111002370	0.000000e+00	5740.0
4	TraesCS5B01G390100	chrUn	86.204	2102	280	6	3769	5860	354151508	354153609	0.000000e+00	2266.0
5	TraesCS5B01G390100	chrUn	87.709	838	57	34	6309	7131	67087726	67086920	0.000000e+00	935.0
6	TraesCS5B01G390100	chrUn	87.709	838	57	34	6309	7131	307431908	307432714	0.000000e+00	935.0
7	TraesCS5B01G390100	chrUn	91.882	271	22	0	948	1218	67087992	67087722	5.480000e-101	379.0
8	TraesCS5B01G390100	chrUn	91.882	271	22	0	948	1218	307431642	307431912	5.480000e-101	379.0
9	TraesCS5B01G390100	chr4D	87.108	5104	615	20	1219	6308	418527977	418522903	0.000000e+00	5740.0
10	TraesCS5B01G390100	chr4D	86.687	5025	625	31	1219	6220	435204070	435199067	0.000000e+00	5533.0
11	TraesCS5B01G390100	chr1A	85.695	5117	672	41	1215	6308	3915032	3920111	0.000000e+00	5339.0
12	TraesCS5B01G390100	chr1A	93.370	920	60	1	1	919	527021979	527022898	0.000000e+00	1360.0
13	TraesCS5B01G390100	chr1A	86.019	844	63	22	6309	7131	559979070	559978261	0.000000e+00	854.0
14	TraesCS5B01G390100	chr1A	84.279	846	57	36	6309	7131	559886660	559885868	0.000000e+00	756.0
15	TraesCS5B01G390100	chr1A	91.447	456	29	4	6309	6757	559941626	559941174	1.070000e-172	617.0
16	TraesCS5B01G390100	chr1A	89.342	319	29	3	6813	7131	559941177	559940864	5.440000e-106	396.0
17	TraesCS5B01G390100	chr1A	91.450	269	23	0	948	1216	559886926	559886658	3.300000e-98	370.0
18	TraesCS5B01G390100	chr1A	90.406	271	26	0	948	1218	559941892	559941622	2.570000e-94	357.0
19	TraesCS5B01G390100	chr4A	84.741	5125	710	43	1219	6308	634259665	634264752	0.000000e+00	5066.0
20	TraesCS5B01G390100	chr4A	84.465	5124	743	44	1219	6308	664327763	664332867	0.000000e+00	5003.0
21	TraesCS5B01G390100	chr4B	84.015	5111	767	31	1219	6309	83843442	83848522	0.000000e+00	4867.0
22	TraesCS5B01G390100	chr5D	86.156	2846	341	19	3479	6308	431886465	431889273	0.000000e+00	3024.0
23	TraesCS5B01G390100	chr5D	86.434	2123	272	15	1216	3329	431883938	431886053	0.000000e+00	2311.0
24	TraesCS5B01G390100	chr5D	90.821	719	30	14	6441	7131	462670009	462670719	0.000000e+00	929.0
25	TraesCS5B01G390100	chr5D	86.078	747	57	27	6309	7048	462746636	462747342	0.000000e+00	760.0
26	TraesCS5B01G390100	chr5D	92.620	271	20	0	948	1218	462669709	462669979	2.530000e-104	390.0
27	TraesCS5B01G390100	chr5D	92.620	271	20	0	948	1218	462746370	462746640	2.530000e-104	390.0
28	TraesCS5B01G390100	chr5D	84.646	254	35	4	7235	7485	462670848	462671100	4.490000e-62	250.0
29	TraesCS5B01G390100	chr5D	83.704	135	16	2	6997	7131	462896901	462897029	1.020000e-23	122.0
30	TraesCS5B01G390100	chr5D	82.653	98	11	3	7140	7233	487170806	487170901	1.730000e-11	82.4
31	TraesCS5B01G390100	chr3D	87.658	1977	236	8	1219	3193	445870713	445868743	0.000000e+00	2292.0
32	TraesCS5B01G390100	chr3D	85.057	87	10	2	7148	7233	551242501	551242417	1.340000e-12	86.1
33	TraesCS5B01G390100	chr1B	94.771	918	47	1	1	918	340425077	340424161	0.000000e+00	1428.0
34	TraesCS5B01G390100	chr1B	72.434	867	206	26	65	919	255514875	255515720	5.800000e-61	246.0
35	TraesCS5B01G390100	chr1B	85.393	89	10	2	7147	7234	415738388	415738302	1.030000e-13	89.8
36	TraesCS5B01G390100	chr1B	83.908	87	11	2	7148	7233	415738303	415738387	6.230000e-11	80.5
37	TraesCS5B01G390100	chr1D	94.583	923	48	2	1	922	223389188	223388267	0.000000e+00	1426.0
38	TraesCS5B01G390100	chr1D	93.182	704	45	3	222	924	223349175	223348474	0.000000e+00	1031.0
39	TraesCS5B01G390100	chr7D	94.559	919	48	2	2	919	88213688	88214605	0.000000e+00	1419.0
40	TraesCS5B01G390100	chr2D	95.407	762	34	1	1	761	467114236	467113475	0.000000e+00	1212.0
41	TraesCS5B01G390100	chr5A	85.565	956	76	26	6589	7488	582654403	582655352	0.000000e+00	944.0
42	TraesCS5B01G390100	chr5A	91.403	221	17	2	6309	6528	582653196	582653415	1.220000e-77	302.0
43	TraesCS5B01G390100	chr5A	87.132	272	22	6	948	1218	582652941	582653200	5.680000e-76	296.0
44	TraesCS5B01G390100	chr3B	81.061	396	45	18	5920	6308	467415845	467416217	9.510000e-74	289.0
45	TraesCS5B01G390100	chr2B	85.714	91	9	3	7148	7237	161464992	161464905	8.000000e-15	93.5
46	TraesCS5B01G390100	chr2B	91.304	69	5	1	854	921	364137670	364137738	8.000000e-15	93.5
47	TraesCS5B01G390100	chr2B	84.043	94	12	2	7148	7240	740308682	740308591	3.720000e-13	87.9
48	TraesCS5B01G390100	chr6A	96.000	50	2	0	871	920	51945167	51945216	1.730000e-11	82.4
49	TraesCS5B01G390100	chr6B	83.908	87	11	2	7148	7233	718384572	718384656	6.230000e-11	80.5

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS5B01G390100	chr5B	569243368	569250855	7487	False	13828.000000	13828	100.000000	1	7488	1	chr5B.!!$F3	7487
1	TraesCS5B01G390100	chr5B	569142191	569149655	7464	False	12454.000000	12454	96.752000	1	7488	1	chr5B.!!$F2	7487
2	TraesCS5B01G390100	chr5B	454865651	454870752	5101	False	5195.000000	5195	85.145000	1219	6308	1	chr5B.!!$F1	5089
3	TraesCS5B01G390100	chrUn	111002370	111007462	5092	True	5740.000000	5740	87.062000	1219	6308	1	chrUn.!!$R1	5089
4	TraesCS5B01G390100	chrUn	354151508	354153609	2101	False	2266.000000	2266	86.204000	3769	5860	1	chrUn.!!$F1	2091
5	TraesCS5B01G390100	chrUn	67086920	67087992	1072	True	657.000000	935	89.795500	948	7131	2	chrUn.!!$R2	6183
6	TraesCS5B01G390100	chrUn	307431642	307432714	1072	False	657.000000	935	89.795500	948	7131	2	chrUn.!!$F2	6183
7	TraesCS5B01G390100	chr4D	418522903	418527977	5074	True	5740.000000	5740	87.108000	1219	6308	1	chr4D.!!$R1	5089
8	TraesCS5B01G390100	chr4D	435199067	435204070	5003	True	5533.000000	5533	86.687000	1219	6220	1	chr4D.!!$R2	5001
9	TraesCS5B01G390100	chr1A	3915032	3920111	5079	False	5339.000000	5339	85.695000	1215	6308	1	chr1A.!!$F1	5093
10	TraesCS5B01G390100	chr1A	527021979	527022898	919	False	1360.000000	1360	93.370000	1	919	1	chr1A.!!$F2	918
11	TraesCS5B01G390100	chr1A	559978261	559979070	809	True	854.000000	854	86.019000	6309	7131	1	chr1A.!!$R1	822
12	TraesCS5B01G390100	chr1A	559885868	559886926	1058	True	563.000000	756	87.864500	948	7131	2	chr1A.!!$R2	6183
13	TraesCS5B01G390100	chr1A	559940864	559941892	1028	True	456.666667	617	90.398333	948	7131	3	chr1A.!!$R3	6183
14	TraesCS5B01G390100	chr4A	634259665	634264752	5087	False	5066.000000	5066	84.741000	1219	6308	1	chr4A.!!$F1	5089
15	TraesCS5B01G390100	chr4A	664327763	664332867	5104	False	5003.000000	5003	84.465000	1219	6308	1	chr4A.!!$F2	5089
16	TraesCS5B01G390100	chr4B	83843442	83848522	5080	False	4867.000000	4867	84.015000	1219	6309	1	chr4B.!!$F1	5090
17	TraesCS5B01G390100	chr5D	431883938	431889273	5335	False	2667.500000	3024	86.295000	1216	6308	2	chr5D.!!$F3	5092
18	TraesCS5B01G390100	chr5D	462746370	462747342	972	False	575.000000	760	89.349000	948	7048	2	chr5D.!!$F5	6100
19	TraesCS5B01G390100	chr5D	462669709	462671100	1391	False	523.000000	929	89.362333	948	7485	3	chr5D.!!$F4	6537
20	TraesCS5B01G390100	chr3D	445868743	445870713	1970	True	2292.000000	2292	87.658000	1219	3193	1	chr3D.!!$R1	1974
21	TraesCS5B01G390100	chr1B	340424161	340425077	916	True	1428.000000	1428	94.771000	1	918	1	chr1B.!!$R1	917
22	TraesCS5B01G390100	chr1B	255514875	255515720	845	False	246.000000	246	72.434000	65	919	1	chr1B.!!$F1	854
23	TraesCS5B01G390100	chr1D	223388267	223389188	921	True	1426.000000	1426	94.583000	1	922	1	chr1D.!!$R2	921
24	TraesCS5B01G390100	chr1D	223348474	223349175	701	True	1031.000000	1031	93.182000	222	924	1	chr1D.!!$R1	702
25	TraesCS5B01G390100	chr7D	88213688	88214605	917	False	1419.000000	1419	94.559000	2	919	1	chr7D.!!$F1	917
26	TraesCS5B01G390100	chr2D	467113475	467114236	761	True	1212.000000	1212	95.407000	1	761	1	chr2D.!!$R1	760
27	TraesCS5B01G390100	chr5A	582652941	582655352	2411	False	514.000000	944	88.033333	948	7488	3	chr5A.!!$F1	6540

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
937	942	2.057137	AATTGTCTGCACACACCACT	57.943	45.000	0.00	0.00	29.76	4.00	F
1770	1811	1.003839	TTCGCCTCCACGCAATCTT	60.004	52.632	0.00	0.00	0.00	2.40	F
3009	3050	0.179111	CATCCGAGCGTGCTTCCTTA	60.179	55.000	0.00	0.00	0.00	2.69	F
3193	3234	0.249405	CAGAAGATGGAGCTCCTCGC	60.249	60.000	32.28	20.62	36.82	5.03	F
4316	4648	0.038455	ACTAGTCCACCTGCTCGAGT	59.962	55.000	15.13	0.00	0.00	4.18	F
4907	5239	0.728466	CGTCGGAGTTGAGGTCGAAC	60.728	60.000	0.00	0.00	33.33	3.95	F
5179	5513	0.762418	TCTCCTTCCCGCAGTTTCAA	59.238	50.000	0.00	0.00	0.00	2.69	F
5895	6236	0.602638	GCCATCTTCACACGTGACCA	60.603	55.000	25.01	1.72	39.66	4.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2225	2266	0.263765	TGACCTTCTAGGCCGGGTAT	59.736	55.000	2.18	0.00	39.63	2.73	R
3200	3241	0.035820	GGATTTCGGCCCGGCATATA	60.036	55.000	12.58	0.00	0.00	0.86	R
4297	4629	0.038455	ACTCGAGCAGGTGGACTAGT	59.962	55.000	13.61	0.00	0.00	2.57	R
4425	4757	0.956633	CAGCCAGTGTGTCTTGCAAT	59.043	50.000	0.00	0.00	37.29	3.56	R
5246	5583	0.831307	GGGAAAGGTACGAGCTGGAT	59.169	55.000	1.44	0.00	0.00	3.41	R
5895	6236	1.023513	GCATCAGAGCTGGTTCGCTT	61.024	55.000	0.00	0.00	41.08	4.68	R
6213	6568	1.269569	CGTCATATAACCCGAGCTGCA	60.270	52.381	1.02	0.00	0.00	4.41	R
6978	8378	1.682702	CCATGGGTGAGCATGCACTAA	60.683	52.381	21.98	3.32	38.78	2.24	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
937	942	2.057137	AATTGTCTGCACACACCACT	57.943	45.000	0.00	0.00	29.76	4.00
1041	1047	2.029666	GTGGTGAGCTGCGAGTGT	59.970	61.111	0.00	0.00	0.00	3.55
1270	1276	2.616960	CGATCACCGGAGATGAAAACA	58.383	47.619	19.75	0.00	33.91	2.83
1275	1281	4.456535	TCACCGGAGATGAAAACAAAAGA	58.543	39.130	9.46	0.00	0.00	2.52
1285	1291	2.341846	AAACAAAAGAGGGTGCGAGA	57.658	45.000	0.00	0.00	0.00	4.04
1286	1292	1.884235	AACAAAAGAGGGTGCGAGAG	58.116	50.000	0.00	0.00	0.00	3.20
1487	1518	2.125106	GATCGGGTCAGGGCACAC	60.125	66.667	0.00	0.00	0.00	3.82
1595	1636	5.838531	AAACCCTAAACATGAACGTGAAA	57.161	34.783	0.00	0.00	0.00	2.69
1770	1811	1.003839	TTCGCCTCCACGCAATCTT	60.004	52.632	0.00	0.00	0.00	2.40
1810	1851	5.126222	TGAGCTCGATGTTCTTCTATCTGTT	59.874	40.000	9.64	0.00	0.00	3.16
2024	2065	1.490910	CAGGTTATCACCCCTCCTTCC	59.509	57.143	0.00	0.00	45.63	3.46
2225	2266	1.606668	GCCTCCATGAAACGTGAAACA	59.393	47.619	0.00	0.00	35.74	2.83
2235	2276	1.078708	CGTGAAACATACCCGGCCT	60.079	57.895	0.00	0.00	35.74	5.19
2552	2593	2.125512	GGTGATCTCCGCTGCGTT	60.126	61.111	21.59	2.43	0.00	4.84
2610	2651	1.374252	GATGAGGCGTGTGGTCGTT	60.374	57.895	0.00	0.00	0.00	3.85
2660	2701	3.372730	GCAGCGCATGAACCCCAA	61.373	61.111	11.47	0.00	0.00	4.12
2717	2758	2.556114	CCCTGGGAGTTTGCTTCAGAAT	60.556	50.000	7.01	0.00	32.11	2.40
2723	2764	5.880332	TGGGAGTTTGCTTCAGAATGTATAC	59.120	40.000	0.00	0.00	37.40	1.47
2725	2766	6.374333	GGGAGTTTGCTTCAGAATGTATACAA	59.626	38.462	10.14	0.00	37.40	2.41
2759	2800	1.004440	GGACGAGGTGCTTCTTGCT	60.004	57.895	0.00	0.00	43.37	3.91
2760	2801	1.016653	GGACGAGGTGCTTCTTGCTC	61.017	60.000	0.00	0.00	43.37	4.26
3009	3050	0.179111	CATCCGAGCGTGCTTCCTTA	60.179	55.000	0.00	0.00	0.00	2.69
3100	3141	0.309302	ATTGTCCTCGATCGAGCTCG	59.691	55.000	34.54	30.03	40.69	5.03
3193	3234	0.249405	CAGAAGATGGAGCTCCTCGC	60.249	60.000	32.28	20.62	36.82	5.03
3200	3241	2.439104	GGAGCTCCTCGCCTGGATT	61.439	63.158	26.25	0.00	40.39	3.01
3288	3329	1.732259	ACCGCATCGAGAACATTGTTC	59.268	47.619	19.64	19.64	0.00	3.18
3329	3370	1.609501	CGAGTTCCACCCCTCCTGA	60.610	63.158	0.00	0.00	0.00	3.86
3331	3372	0.545548	GAGTTCCACCCCTCCTGAGT	60.546	60.000	0.00	0.00	0.00	3.41
3355	3396	3.315142	GACGCTGGAGTGGATGGCA	62.315	63.158	0.00	0.00	0.00	4.92
3373	3414	0.946221	CACTGGAGTTGACGGTGCTC	60.946	60.000	0.00	0.00	38.27	4.26
3705	4009	1.069022	CCCTTCACATGCACGAAACAG	60.069	52.381	0.00	0.00	0.00	3.16
3874	4178	0.971447	GGCCTTCAGTAGACTCCGGT	60.971	60.000	0.00	0.00	0.00	5.28
4297	4629	3.725459	CAGGCATGCGTCGCACAA	61.725	61.111	24.34	0.00	43.04	3.33
4316	4648	0.038455	ACTAGTCCACCTGCTCGAGT	59.962	55.000	15.13	0.00	0.00	4.18
4425	4757	4.678499	TGTCGCCATCGCTGTGCA	62.678	61.111	0.00	0.00	35.26	4.57
4489	4821	1.218316	GACGATTCGGTGCTCCCTT	59.782	57.895	11.29	0.00	0.00	3.95
4549	4881	2.107041	AACACGCCGTCCTGGATCAA	62.107	55.000	0.00	0.00	42.00	2.57
4604	4936	3.665675	GATTCTGTGGGAGCGCGGT	62.666	63.158	12.23	12.23	0.00	5.68
4701	5033	2.537792	GATGTTGACGACGGAGCCGA	62.538	60.000	16.83	0.00	42.83	5.54
4739	5071	2.338620	CTGACGGCCGTGTTGAGA	59.661	61.111	39.65	10.95	0.00	3.27
4907	5239	0.728466	CGTCGGAGTTGAGGTCGAAC	60.728	60.000	0.00	0.00	33.33	3.95
5035	5368	2.476051	CGCCTGTTTGCAGTAGCG	59.524	61.111	4.68	4.68	46.23	4.26
5179	5513	0.762418	TCTCCTTCCCGCAGTTTCAA	59.238	50.000	0.00	0.00	0.00	2.69
5189	5523	1.789739	CAGTTTCAAGCGCGCGAAG	60.790	57.895	37.18	21.81	0.00	3.79
5895	6236	0.602638	GCCATCTTCACACGTGACCA	60.603	55.000	25.01	1.72	39.66	4.02
6213	6568	6.648310	GCTAAAACCTCTAACTAAACCGAGTT	59.352	38.462	0.00	0.00	42.35	3.01
6978	8378	6.169094	CAGAAACATGAGAGGTTGATACTGT	58.831	40.000	0.00	0.00	0.00	3.55
7279	8726	4.554960	AAGTACTCCACTTAGCTTTCCC	57.445	45.455	0.00	0.00	45.93	3.97
7396	8843	4.461431	CCCCTCTAATTTTTGTTAGCCGTT	59.539	41.667	0.00	0.00	32.85	4.44

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
926	931	0.663153	GTCCTTTGAGTGGTGTGTGC	59.337	55.000	0.00	0.00	0.00	4.57
937	942	1.609208	GGCTCTGCTTTGTCCTTTGA	58.391	50.000	0.00	0.00	0.00	2.69
1050	1056	2.681778	CCGGTGCACTCCTCCTCT	60.682	66.667	17.98	0.00	0.00	3.69
1081	1087	1.296715	CAAAGTAGGCCCTCACGCT	59.703	57.895	0.00	0.00	0.00	5.07
1270	1276	1.548269	CTCTCTCTCGCACCCTCTTTT	59.452	52.381	0.00	0.00	0.00	2.27
1275	1281	0.107214	CTCTCTCTCTCTCGCACCCT	60.107	60.000	0.00	0.00	0.00	4.34
1285	1291	1.067213	GCGCAAAAGGTCTCTCTCTCT	60.067	52.381	0.30	0.00	0.00	3.10
1286	1292	1.067213	AGCGCAAAAGGTCTCTCTCTC	60.067	52.381	11.47	0.00	0.00	3.20
1487	1518	6.695429	ACTCGGTTTAGTTAGAGGTTTTAGG	58.305	40.000	0.00	0.00	35.22	2.69
1595	1636	2.385417	AGGGGGTGATTGTTGGGTAAAT	59.615	45.455	0.00	0.00	0.00	1.40
1770	1811	4.517285	GAGCTCAGGTACCATTTCATCAA	58.483	43.478	15.94	0.00	0.00	2.57
1810	1851	2.229543	GCAAAGAATCCTGTGATGCACA	59.770	45.455	0.00	0.00	42.45	4.57
2024	2065	2.620112	CGGCACCCTGTTCTTGCTG	61.620	63.158	0.00	0.00	36.46	4.41
2225	2266	0.263765	TGACCTTCTAGGCCGGGTAT	59.736	55.000	2.18	0.00	39.63	2.73
2235	2276	0.970937	CGCCCTGACCTGACCTTCTA	60.971	60.000	0.00	0.00	0.00	2.10
2552	2593	4.081142	ACGACCTGGTGATCATTGTATCAA	60.081	41.667	2.82	0.00	37.61	2.57
2610	2651	4.973055	GTGTACGCACGGGGCACA	62.973	66.667	1.92	0.00	45.17	4.57
2650	2691	2.242043	CTTGAGCAAGTTGGGGTTCAT	58.758	47.619	4.75	0.00	33.87	2.57
2759	2800	1.890041	CCAGGGTTTGTCGTTGCGA	60.890	57.895	0.00	0.00	0.00	5.10
2760	2801	2.637025	CCAGGGTTTGTCGTTGCG	59.363	61.111	0.00	0.00	0.00	4.85
2995	3036	3.532542	AGGTAAATAAGGAAGCACGCTC	58.467	45.455	0.00	0.00	0.00	5.03
3003	3044	6.502863	AGTGGGTCTACAAGGTAAATAAGGAA	59.497	38.462	0.00	0.00	0.00	3.36
3009	3050	5.280521	CCTGAAGTGGGTCTACAAGGTAAAT	60.281	44.000	0.00	0.00	0.00	1.40
3100	3141	1.587547	GGAGCCATGATCGAAGAACC	58.412	55.000	0.00	0.00	43.58	3.62
3193	3234	0.394352	GGCCCGGCATATAATCCAGG	60.394	60.000	12.58	0.00	0.00	4.45
3200	3241	0.035820	GGATTTCGGCCCGGCATATA	60.036	55.000	12.58	0.00	0.00	0.86
3288	3329	1.361668	CTCCACCGACGCCATTCAAG	61.362	60.000	0.00	0.00	0.00	3.02
3329	3370	2.345244	CTCCAGCGTCTGCCAACT	59.655	61.111	1.84	0.00	44.31	3.16
3331	3372	2.031012	CACTCCAGCGTCTGCCAA	59.969	61.111	1.84	0.00	44.31	4.52
3355	3396	1.367840	GAGCACCGTCAACTCCAGT	59.632	57.895	0.00	0.00	0.00	4.00
3373	3414	1.734477	CTCCAGCGTCGTTGTCTGG	60.734	63.158	8.32	9.03	46.60	3.86
3558	3861	1.717348	CGTGCACATCACATGCGAT	59.283	52.632	18.64	0.00	46.49	4.58
3705	4009	2.158561	ATTTCCTGCGCACCTTTGGC	62.159	55.000	5.66	0.00	0.00	4.52
3754	4058	1.003839	ACGGCATGACACCATTCGT	60.004	52.632	0.00	0.00	36.18	3.85
3874	4178	1.227102	GCATAGTGGTGGGCATGGA	59.773	57.895	0.00	0.00	0.00	3.41
4297	4629	0.038455	ACTCGAGCAGGTGGACTAGT	59.962	55.000	13.61	0.00	0.00	2.57
4425	4757	0.956633	CAGCCAGTGTGTCTTGCAAT	59.043	50.000	0.00	0.00	37.29	3.56
4489	4821	1.068055	GTCGTCTTCTCGCCAAGGTAA	60.068	52.381	0.00	0.00	0.00	2.85
4531	4863	2.579657	TTGATCCAGGACGGCGTGT	61.580	57.895	21.19	0.02	33.14	4.49
4532	4864	2.100631	GTTGATCCAGGACGGCGTG	61.101	63.158	21.19	3.34	33.14	5.34
4549	4881	2.203907	AGAGAGGCTGCCAGGTGT	60.204	61.111	22.65	0.00	0.00	4.16
4604	4936	1.332144	GGGTGTACTACATCCCGCCA	61.332	60.000	7.22	0.00	43.62	5.69
5035	5368	5.309638	GGGAAAAGTCTAAGGATATCTGCC	58.690	45.833	2.05	0.00	0.00	4.85
5189	5523	1.251527	TTCTCACGGAGGAGGAGTGC	61.252	60.000	1.76	0.00	35.97	4.40
5246	5583	0.831307	GGGAAAGGTACGAGCTGGAT	59.169	55.000	1.44	0.00	0.00	3.41
5279	5616	3.532155	GAGGAGCTCATCGGGCGT	61.532	66.667	17.19	0.00	34.52	5.68
5748	6086	1.728074	CTGACGCGCACGAACTACA	60.728	57.895	5.73	0.00	43.93	2.74
5895	6236	1.023513	GCATCAGAGCTGGTTCGCTT	61.024	55.000	0.00	0.00	41.08	4.68
6213	6568	1.269569	CGTCATATAACCCGAGCTGCA	60.270	52.381	1.02	0.00	0.00	4.41
6978	8378	1.682702	CCATGGGTGAGCATGCACTAA	60.683	52.381	21.98	3.32	38.78	2.24

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.